Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013855.1 Kokia drynarioides strain JFW-HI SEQ_128883, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6678
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:1654 original size:17 final size:17
Alignment explanation
Indices: 1619--1652 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1609 TAAGATGACT
*
1619 ATAAAAAATTTTAATAA
1 ATAAAAAATTTGAATAA
1636 ATAAAAAA-TTGAATAA
1 ATAAAAAATTTGAATAA
1652 A
1 A
1653 ATTATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
ATAAAAAATTTGAATAA
Found at i:1683 original size:20 final size:21
Alignment explanation
Indices: 1647--1685 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1637 TAAAAAATTG
*
1647 AATAAAATTATTAAATATTAA
1 AATAAAATTAATAAATATTAA
1668 AATAAAA-TAATAAATATT
1 AATAAAATTAATAAATATT
1686 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AATAAAATTAATAAATATTAA
Found at i:3875 original size:60 final size:60
Alignment explanation
Indices: 3715--3875 Score: 191
Period size: 60 Copynumber: 2.6 Consensus size: 60
3705 ACCCGGGGGT
* * * * *
3715 AAAATGATAATTTTGGAC-TCTCGGGGTAAAACGGTAATTTTTAGAAAAAAAATCAAGATCAA
1 AAAATGA-ATTTTTGGACATCTGGGGGTAAAAAGGTAATTCTTAG--AAAAAATCAAGATAAA
* * * *
3777 AAAATGAATTTTTGGACATTTGGGGGTGAAATGTTAATTCTTAG-AAAAATCAAGATAAA
1 AAAATGAATTTTTGGACATCTGGGGGTAAAAAGGTAATTCTTAGAAAAAATCAAGATAAA
3836 AAAATGGAATTTTTGGACATCTGGGGGTAAAAAGGTAATT
1 AAAAT-GAATTTTTGGACATCTGGGGGTAAAAAGGTAATT
3876 TTCAAAAGTT
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
59 19 0.22
60 30 0.35
61 9 0.11
62 27 0.32
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (60 bp):
AAAATGAATTTTTGGACATCTGGGGGTAAAAAGGTAATTCTTAGAAAAAATCAAGATAAA
Found at i:3920 original size:58 final size:57
Alignment explanation
Indices: 3836--4086 Score: 238
Period size: 58 Copynumber: 4.3 Consensus size: 57
3826 TCAAGATAAA
* * ** *
3836 AAAATGGAATTTTTGGACATCTGGGGGTAAAAAGGTAATTTTCAAAAGTTACGGGGTC
1 AAAATGGAATTTTTGGACATCCGGGGG-AAAATGGTAATTTTTGAAAGTTTCGGGGTC
* * * *
3894 AAAATGGAATTTTTGGACATCCGGGGGCAAATGGAAATTTTTGAAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGACATCCGGGGGAAAATGGTAATTTTTGAAAGTTTCG-GGGTC
* **
3952 AAAATGGAATTTTTGGACATCCGGGGGCAAAATGAT-ATTTTTGAAAGTTTTAGGGTC
1 AAAATGGAATTTTTGGACATCCGGGGG-AAAATGGTAATTTTTGAAAGTTTCGGGGTC
* ** * * *
4009 AAAAATGGAATTTTTGGA-AGTTCAGGGTTAAAAAT-GTAATTTTTGGAAGTTTTAGGGGTTA
1 -AAAATGGAATTTTTGGACA--TCCGGG-GGAAAATGGTAATTTTTGAAAG-TTTCGGGG-TC
4070 AAAATGGAATTTTTGGA
1 AAAATGGAATTTTTGGA
4087 AGTTTGGGGG
Statistics
Matches: 160, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
57 23 0.14
58 88 0.55
59 25 0.16
60 23 0.14
61 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (57 bp):
AAAATGGAATTTTTGGACATCCGGGGGAAAATGGTAATTTTTGAAAGTTTCGGGGTC
Found at i:3991 original size:28 final size:28
Alignment explanation
Indices: 3836--3994 Score: 101
Period size: 28 Copynumber: 5.5 Consensus size: 28
3826 TCAAGATAAA
* *
3836 AAAATGGAATTTTTGGACATCTGGGGGT
1 AAAATGGAATTTTTGGACATCCGGGGGC
* ** * * *
3864 AAAAAGGTAA-TTTTCAAAAGTTACGGGGTC
1 AAAATGG-AATTTTTGGACA--TCCGGGGGC
3894 AAAATGGAATTTTTGGACATCCGGGGGC
1 AAAATGGAATTTTTGGACATCCGGGGGC
* * ***
3922 -AAATGGAAATTTTT-GAAAGTTTCGAGGTTA
1 AAAATGG-AATTTTTGGACA--TCCG-GGGGC
3952 AAAATGGAATTTTTGGACATCCGGGGGC
1 AAAATGGAATTTTTGGACATCCGGGGGC
3980 AAAAT-GATATTTTTG
1 AAAATGGA-ATTTTTG
3995 AAAGTTTTAG
Statistics
Matches: 96, Mismatches: 24, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
27 11 0.11
28 40 0.42
29 10 0.10
30 26 0.27
31 9 0.09
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (28 bp):
AAAATGGAATTTTTGGACATCCGGGGGC
Found at i:4112 original size:29 final size:29
Alignment explanation
Indices: 3835--4104 Score: 178
Period size: 29 Copynumber: 9.2 Consensus size: 29
3825 ATCAAGATAA
*
3835 AAAAATGGAATTTTTGGACA-TCTGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTTGGGGGT
*** **
3864 AAAAA-GGTAATTTTCAAAAGTTACGGGGT
1 AAAAATGG-AATTTTTGGAAGTTTGGGGGT
* **
3893 CAAAATGGAATTTTTGGACA-TCCGGGGG-
1 AAAAATGGAATTTTTGGA-AGTTTGGGGGT
* * * *
3921 -CAAATGGAAATTTTTGAAAGTTTCGAGGTT
1 AAAAATGG-AATTTTTGGAAGTTT-GGGGGT
**
3951 AAAAATGGAATTTTTGGACA-TCCGGGGG-
1 AAAAATGGAATTTTTGGA-AGTTTGGGGGT
* * **
3979 CAAAAT-GATATTTTTGAAAGTTTTAGGGT
1 AAAAATGGA-ATTTTTGGAAGTTTGGGGGT
** *
4008 CAAAAATGGAATTTTTGGAAGTTCAGGGTT
1 -AAAAATGGAATTTTTGGAAGTTTGGGGGT
* *
4038 AAAAATGTAATTTTTGGAAGTTTTAGGGGTT
1 AAAAATGGAATTTTTGGAAG-TTT-GGGGGT
4069 AAAAATGGAATTTTTGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
4098 AAAAATG
1 AAAAATG
4105 TAAATTTTAA
Statistics
Matches: 182, Mismatches: 42, Indels: 34
0.71 0.16 0.13
Matches are distributed among these distances:
27 10 0.05
28 30 0.16
29 71 0.39
30 38 0.21
31 33 0.18
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGGT
Found at i:5125 original size:9 final size:9
Alignment explanation
Indices: 5113--5191 Score: 61
Period size: 9 Copynumber: 8.7 Consensus size: 9
5103 TAATATTTAA
5113 TATTAATAT
1 TATTAATAT
5122 TATTAATAT
1 TATTAATAT
* *
5131 CATTATTAT
1 TATTAATAT
*
5140 TAATTAATAC
1 T-ATTAATAT
* *
5150 CATTAGTAT
1 TATTAATAT
*
5159 TA-TACTTAT
1 TATTA-ATAT
5168 TATTAATAT
1 TATTAATAT
*
5177 TATTATTAT
1 TATTAATAT
*
5186 CATTAA
1 TATTAA
5192 GGCTATTTAT
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
8 2 0.04
9 43 0.81
10 8 0.15
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (9 bp):
TATTAATAT
Found at i:5138 original size:3 final size:3
Alignment explanation
Indices: 5113--5190 Score: 50
Period size: 3 Copynumber: 25.7 Consensus size: 3
5103 TAATATTTAA
* * * * * * *
5113 TAT TAA TAT TAT TAA TAT CAT TAT TAT TAAT TAA TAC CAT TAG TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
* *
5159 TA- TACT TAT TAT TAA TAT TAT TAT TAT CAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA
5191 AGGCTATTTA
Statistics
Matches: 55, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
2 2 0.04
3 48 0.87
4 5 0.09
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (3 bp):
TAT
Found at i:5147 original size:19 final size:19
Alignment explanation
Indices: 5114--5160 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5104 AATATTTAAT
*
5114 ATTAATATT-ATTAATATC
1 ATTAATATTAATTAATACC
*
5132 ATTATTATTAATTAATACC
1 ATTAATATTAATTAATACC
*
5151 ATTAGTATTA
1 ATTAATATTA
5161 TACTTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTAATATTAATTAATACC
Found at i:5889 original size:6 final size:6
Alignment explanation
Indices: 5880--5975 Score: 78
Period size: 6 Copynumber: 16.7 Consensus size: 6
5870 TTTAGACATT
* *
5880 AATTTA AATTTA AATTTA AACTTA AATTTA TAA--TA AATTTA AATTTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * * *
5927 AA-GTA AATTTA AACTTA AA-ATA AATTT- AATTTGA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
5972 AATT
1 AATT
5976 CTGTTGGGCC
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
4 2 0.03
5 17 0.24
6 48 0.68
7 4 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:5890 original size:18 final size:16
Alignment explanation
Indices: 5863--5975 Score: 66
Period size: 17 Copynumber: 6.6 Consensus size: 16
5853 GGACACTTGT
*
5863 ATTTATATTTAGACATTA
1 ATTTAAATTTA-A-ATTA
5881 ATTTAAATTTAAATTTAA
1 ATTTAAATTTAAA-TT-A
* *
5899 ACTTAAATTTATAATAA
1 ATTTAAATTTA-AATTA
* *
5916 ATTTAAATTTTAAGTAA
1 ATTTAAA-TTTAAATTA
* *
5933 ATTTAAACTTAAAATAA
1 ATTTAAA-TTTAAATTA
*
5950 ATTT-AATTTGAAAATAA
1 ATTTAAATTT--AAATTA
5967 ATTTAAATT
1 ATTTAAATT
5976 CTGTTGGGCC
Statistics
Matches: 79, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
15 2 0.03
16 3 0.04
17 42 0.53
18 30 0.38
19 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
ATTTAAATTTAAATTA
Found at i:5916 original size:17 final size:17
Alignment explanation
Indices: 5880--5975 Score: 113
Period size: 17 Copynumber: 5.6 Consensus size: 17
5870 TTTAGACATT
*
5880 AATTTAAATTTAAATTTA
1 AATTTAAATTTAAA-ATA
* *
5898 AACTTAAATTTATAATA
1 AATTTAAATTTAAAATA
* *
5915 AATTTAAATTTTAAGTA
1 AATTTAAATTTAAAATA
*
5932 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
5949 AATTT-AATTTGAAAATA
1 AATTTAAATTT-AAAATA
5966 AATTTAAATT
1 AATTTAAATT
5976 CTGTTGGGCC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
16 4 0.06
17 45 0.69
18 16 0.25
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:6546 original size:134 final size:133
Alignment explanation
Indices: 6302--6556 Score: 359
Period size: 134 Copynumber: 1.9 Consensus size: 133
6292 GGTTTCATTG
* ** **
6302 ACTTGACCTTCTTCTCAATATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTC
1 ACTTGACCTGCTTCTCAATATCTCATCAGGAAGATGACAACATCACTTGTTTCAATCCACTTCTC
* * * *
6367 TATGTTTCATCAGGAAGACGGATTTGATTCACTTCTCCGTATCTCATCAGGAAGCTAACTACTTT
66 TATGTTTCATCAGGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAAGAAGCTAACTACTTT
6432 ATT
131 ATT
* * *
6435 ACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGATGACAACATCGCTTGTTTCAATCCGCTTCT
1 ACTT-GACCTGCTTCTCAATATCTCATCAGGAAGATGACAACATCACTTGTTTCAATCCACTTCT
* *
6500 CTGT-TTCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCT
65 CTATGTT-TCATCAGGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAAGAAGCT
6557 GGGATTCAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
133 6 0.06
134 100 0.94
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (133 bp):
ACTTGACCTGCTTCTCAATATCTCATCAGGAAGATGACAACATCACTTGTTTCAATCCACTTCTC
TATGTTTCATCAGGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAAGAAGCTAACTACTTT
ATT
Done.